IMAP-VISUALIZATION

Exploratory Analysis of 16S-Based Microbial Profiles

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

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Microbiome Data Visualization

Overview of Snakemake workflow

Heatmaps

Using qiime2R

Using ggplot

Bray-Curtis

Jaccard

Bray-Curtis and Jaccard

Using microViz

No group annotation

With group annotation at the bottom

Jitter plots

Line plots

PCoA ordination

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using MOTHUR and Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 and Snakemake workflows	In-progress
IMAP-PART 07	Processing Output from 16S-Based microbiome bioinformatics pipelines	In-progress
IMAP-PART 08	Exploratory Analysis of 16S-Based Microbiome Processed Data	In-progress
IMAP-PART 09	Visualization of Microbiome Data with the integration of Snakemake Workflows	In-progress
IMAP-PART XX	Predictive Modeling of Microbiome Data Using Machine Learning Techniques	In-progress
IMAP-SUMMARY	Summary of snakemake workflows for microbiome data analysis	In-progress

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── Rplots.pdf
├── config
│   └── config.yml
├── css
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature_table.qza
│   ├── features.csv
│   ├── metadata.csv
│   ├── processed_data.rda
│   ├── processed_objects.rda
│   ├── rooted_tree.qza
│   ├── sample_metadata.tsv
│   ├── shannon.csv
│   ├── shannon_vector.qza
│   ├── taxonomy.csv
│   ├── taxonomy.qza
│   └── unweighted_unifrac_pcoa.qza
├── figures
│   ├── ggplot_heatmap.png
│   ├── ggplot_heatmap.svg
│   ├── microviz_heatmap.png
│   ├── microviz_heatmap.svg
│   ├── q2r_barplot.png
│   ├── q2r_barplot.svg
│   ├── q2r_heatmap.png
│   ├── q2r_heatmap.svg
│   ├── q2r_jitterplot.png
│   ├── q2r_jitterplot.svg
│   ├── q2r_lineplot.png
│   ├── q2r_lineplot.svg
│   ├── q2r_pcoa.png
│   ├── q2r_pcoa.svg
│   ├── unnamed-chunk-1-1.png
│   ├── unnamed-chunk-2-1.png
│   ├── unnamed-chunk-3-1.png
│   ├── unnamed-chunk-4-1.png
│   ├── unnamed-chunk-5-1.png
│   ├── unnamed-chunk-6-1.png
│   └── unnamed-chunk-7-1.png
├── images
│   ├── bkgd.png
│   ├── coders.png
│   ├── ml.png
│   ├── smkreport
│   │   └── screenshot.png
│   └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   ├── packages.bib
│   └── references.bib
├── report.html
├── results
│   └── project_tree.txt
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   └── environment.yml
    ├── report
    │   ├── barplot.rst
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmap.rst
    │   ├── jitterplot.rst
    │   ├── lineplot.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoa.rst
    │   ├── scatter.rst
    │   ├── venndiagram.rst
    │   ├── volcano.rst
    │   └── workflow.rst
    ├── rules
    │   ├── barplot.smk
    │   ├── gh_pages.smk
    │   ├── heatmap.smk
    │   ├── jitter.smk
    │   ├── lineplot.smk
    │   ├── pcoa.smk
    │   ├── processed_data.smk
    │   ├── project_tree.smk
    │   ├── rulegraph.smk
    │   ├── smk_report.smk
    │   ├── venn.smk
    │   └── visual_types.smk
    └── scripts
        ├── README.md
        ├── alpha.R
        ├── barplot.R
        ├── build_bs4_book.bash
        ├── common.R
        ├── custom_theme.R
        ├── heatmap.R
        ├── jitterplot.R
        ├── lefse.R
        ├── lineplot.R
        ├── pcoa.R
        ├── processed_data.R
        ├── qiime2R.R
        ├── qiime2csv.R
        ├── rarefy.R
        ├── read_matrix.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        ├── tree.sh
        └── volcanoplot.R

14 directories, 102 files

Troubleshooting of FAQs

1. Question
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2. Question
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Last updated on May 09, 2023.
Github_Repo: https://github.com/tmbuza/imap-data-visualization.
Repo compiled and maintained by: Teresia Mrema-Buza.